ArticleNucleic acids research2018
PULDB: the expanded database of Polysaccharide Utilization Loci.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
168 citing papers in PubMed.
- Controlled colonization of the human gut with a genetically engineered microbial therapeutic.Science (New York, N.Y.) · 2025Trial
- Trial
- Microbial enterotypes beyond genus level:Gut microbes · 2020Trial
- High-throughput analyses ofGut microbes · 2026Article
- Structural characterization of an α-glucosaccharide-binding protein fromJournal of structural biology: X · 2026Article
- Structural and functional characterisation of the dextran utilisome fromJournal of structural biology: X · 2026Article
- Exploration of Alkaliphilic Bacteria Alkalitalea saponilacus Identifies Glycoside Hydrolases With Biotechnological Potential.Microbial biotechnology · 2026Article
- Extracellular metabolite production byApplied and environmental microbiology · 2026Article
- Enzymatic tools for the treatment of caries-associated biofilms: Investigating the enzymes of a putative polysaccharide utilization locus from Prevotella melaninogenica and their application against Streptococcus mutans biofilm.World journal of microbiology & biotechnology · 2026Article
- Alginate foraging is conserved in geographically and taxonomically distinct ruminant microbiomes.Nature communications · 2026Article
- Predicting functions of uncharacterized gene products from microbial communities.Nature biotechnology · 2026Article
- Constitutive activation of a hybrid two-component regulator reveals cross-regulation of polysaccharide utilization genes in Bacteroides.The Journal of biological chemistry · 2026Article
- Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes.bioRxiv : the preprint server for biology · 2026Article
- Strategies for GH functional annotation: toward harmonized and predictive CAZymology.Biotechnology for biofuels and bioproducts · 2026Article
- A system for transferring large genetic loci inApplied and environmental microbiology · 2026Article
- Unusual molecular architecture of a human gut microbiota β-mannanase reveals a new CBM family.Cellular and molecular life sciences : CMLS · 2026Article
- Dissecting a two-domain alginate lyase of family PL6 reveals a mechanistic basis for substrate specificity and enzyme activity.The Journal of biological chemistry · 2026Article
- Structural and functional insights into Uly1040, an ulvan lyase from polysaccharide lyase family 40.Applied and environmental microbiology · 2026Article
- Cross-feeding interactions betweenmSystems · 2026Article
- Revisiting Hyaluronan Catabolism in Bacteroides: Pathway Conservation, Overlooked Proteins, and Predictive Accuracy.MicrobiologyOpen · 2026Article
108 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
The Polysaccharide Utilization Loci (PUL) database was launched in 2015 to present PUL predictions in ∼70 Bacteroidetes species isolated from the human gastrointestinal tract, as well as PULs derived from the experimental data reported in the literature. In 2018 PULDB offers access to 820 genomes, sampled from various environments and covering a much wider taxonomical range. A Krona dynamic chart was set up to facilitate browsing through taxonomy. Literature surveys now allows the presentation of the most recent (i) PUL repertoires deduced from RNAseq large-scale experiments, (ii) PULs that have been subjected to in-depth biochemical analysis and (iii) new Carbohydrate-Active enzyme (CAZyme) families that contributed to the refinement of PUL predictions. To improve PUL visualization and genome browsing, the previous annotation of genes encoding CAZymes, regulators, integrases and SusCD has now been expanded to include functionally relevant protein families whose genes are significantly found in the vicinity of PULs: sulfatases, proteases, ROK repressors, epimerases and ATP-Binding Cassette and Major Facilitator Superfamily transporters. To cope with cases where susCD may be absent due to incomplete assemblies/split PULs, we present 'CAZyme cluster' predictions. Finally, a PUL alignment tool, operating on the tagged families instead of amino-acid sequences, was integrated to retrieve PULs similar to a query of interest. The updated PULDB website is accessible at www.cazy.org/PULDB_new/.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.